You never know where a scientific exploration will take you – I learned so much about so many different things just by researching single amino acids, and Asparagine (Asn, N) turns out to be one of those story-starters. Yes, the name does come from asparagus, but that’s not the big story I want to tell you about. Today is ALL about Asn & how childhood Acute Lymphoblastic Leukemia (ALL) has an “Achille’s heel” for it that is targeted in mainstay treatment.  

refreshed & video added 12/17/21

It’s Day 17 of #20DaysOfAminoAcids – the bumbling biochemist’s version of an advent calendar. Amino acids are the building blocks of proteins. There are 20 (common) genetically-specified ones, each with a generic backbone with to allow for linking up through peptide bonds to form chains (polypeptides) that fold up into functional proteins, as well as unique side chains (aka “R groups” that stick off like charms from a charm bracelet). Each day I’m going to bring you the story of one of these “charms” – what we know about it and how we know about it, where it comes from, where it goes, and outstanding questions nobody knows. ⠀

More on amino acids in general here but the basic overview is: amino acids have generic “amino” (NH₃⁺/NH₂) & “carboxyl” (COOH/COO⁻) groups that let them link up together through peptide bonds (N links to C, H₂O lost, and the remaining “residual” parts are called residues). The reason for the “2 options” in parentheses is that these groups’ protonation state (how many protons (H⁺ ) they have) depends on the pH (which is a measure of how many free H⁺ are around to take).⠀

Those generic parts are attached to a central “alpha carbon” (Ca), which is also attached to one of 20 unique side chains (“R groups”) which have different properties (big, small, hydrophilic (water-loving), hydrophobic (water-avoided), etc.) & proteins have different combos of them, so the proteins have different properties. And we can get a better appreciation and understanding of proteins if we look at those letters. So, today let’s look at Asparagine (Asn, N).

Asparagine (Asn, N) is the “cousin” to the amino acid we looked at yesterday – Aspartate (Asp, D). 

Unlike Asp, which is negatively-charged under usual bodily (physiological) conditions, asparagine is neutral. But they look a lot alike – and as we’ll see, our bodies can convert between the two of them. Both have a methylene (-CH₂) followed by a carbonyl (C=O) in their side chain, but they differ in what’s attached to that carbonyl C on the other side. Asp has another O, giving it a “carboxyl group” but Asn has an amino group (-NH₂) instead. This makes Asn the AMIDE of Asp. AM I DEscribing something without defining the jargon? I’ll fix that – and tell you more about Asn biochemistry – after I tell you a story about it (don’t worry, you don’t need to know the nomenclature stuff for it)). 

Asparagine is considered nonessential in the dietary sense of the word – our bodies can make it. But they can also break it, and they can use it to build other molecules (this can be joining up with other peptides to form big ole proteins, or getting modified to form other small molecules). So the levels of free Asn in your body at any time depend on how much of it you eat, how much you make, how much you break, & how much you “siphon away.” Your body keeps a nice balance by regulating the making, breaking, and other-purpose-using. 

In a type of blood cancer called childhood Acute Lymphoblastic Leukemia (ALL), the balance gets thrown off because the cells lose their ability to make it as much, but they still need it, so they rely on a steady source of “pre-made” Asn from the bloodstream. This has led to a therapeutic strategy of depriving these cells of what little Asp they do have by adding extra “breakers” into the bloodstream, depleting the Asn supply – this strategy selectively affects the cancer cells because the other cells have enough “makers” to counterbalance these “breakers”

So let’s meet these molecular workers, which have the general job description of “enzymes.” An enzyme is a reaction-speed-upper – it’s usually a protein, sometimes a protein/RNA combo, sometimes RNA alone, and it helps mediate reactions by doing things like bringing reactants together and holding them in the right orientation with the right ambience, etc. You know you’re probably dealing with an enzyme if you see the ending “-ase” 

The “maker” is an enzyme called Asparagine Synthetase (ASNS) and it makes Asn through a “transamination” reaction which transfers an amino group from the amino acid glutamine to aspartate, turning aspartate into asparagine and glutamine into glutamate. It has a pretty cool reaction  – I won’t bore you too much, but it has a mechanism involving 2 “active sites” (places where reactions occur). It requires spending a molecule of ATP to “activate” the carboxylate group in Asp’s side chain that you want to turn into an amide. First the carboxylate attacks ATP’s innermost phosphate group, kicking off 2 of the phosphates as inorganic (non-carbon-attached) pyrophosphate (PPi), and leaving you with a β-aspartyl-AMP intermediate where Asp has AMP stuck to it as a big ole, energetically unstable, “attack here” sign. Meanwhile, in the enzyme’s second active site, the amine group is cut off from glutamine as ammonia (NH₃), which travels through a secret tunnel between the active sites to attack, releasing AMP & swapping it out for an amino group.

The “breaker” is an enzyme called Asparaginase (ASNase). It catalyzes the splitting up of Asn into aspartate and ammonia. When Asn is broken down for energy, it follows the usual “remove amino parts & process them and the carbon skeletons separately” routine we’ve seen. But, unlike most of the other amino acids, we have 2 amino groups to remove. ASNase does the first removal – that of the “extra” amino group – the side chain one, to give you aspartate. And then that aspartate gets broken down the same way aspartate does – because it *is* aspartate now! The backbone amino group is removed by aspartate aminotransferase to give you OXALOACETATE, which is nitrogen-free and can get processed in the citric acid cycle (aka TCA, aka Krebs cycle) to get energy. Alternatively, the Asp can be used as Asp. 

It’s the ASNase that’s used as an anti-cancer treatment – and the version that’s used as a drug comes from bacteria – as a biochemist, I’m really used to the concept of using bacterial proteins to do things for us – like using bacterial “restriction enzymes” (site-specific endonucleases) to recognize and cut specific DNA sequences. When I’m using bacterial proteins, it’s in a test tube, (in vitro) but turns out bacterial enzymes can be used in people too (in vivo). Including to treat childhood Acute Lymphoblastic Leukemia.

“Leukemia” is an umbrella term for cancers that affect blood & bone marrow (where blood cells are made). There are different types of leukemia that affect different types of blood cells – ALL affects lymphoid progenitor cells (a type of white blood cell important for the immune system) and can cause problems including anemia, fatigue, and immune system dysfunction. First tried out in the 1960s (more on the history below), E. coli ASNase has become a mainstay of treatment for childhood ALL – in addition to traditional chemotherapy drugs like vincristine & prednisone, patients are given this enzyme, and here’s why it *hopefully* works.

Both normal and cancer lymphocytes need Asn – and they get their supply by taking it in from circulating blood plasma (plasma is just the non-cell part of the blood). When you introduce ASNase into the blood, it goes to work breaking the Asn down, depleting this supply. This causes leukemic blasts to actually start shipping their cytoplasmic stock out (which gets broken down), so they get depleted intracellularly. And, unlike normal cells, these cancer cells aren’t able to make much if any of their own because, for reasons still not fully understood, they don’t make much of the “maker,” ASNS. But they need Asn to build proteins and survive – and now they can’t get it from the blood & they can’t make it, so they die off. But the normal cells are fine because they *do* express ASNS & therefore they can make enough to compensate for what they can’t get “pre-made” from the bloodstream. 

ASNase also depletes the glutamine pool because, even though ASNase prefers breaking down Asn, it can also deaminate glutamine (into glutamate & ammonia). So now you’re messing with levels of multiple amino acids. One of the coolest things about metabolism is that it’s like the “7 degrees to Kevin Bacon” thing – all molecules seem to be somehow connected. But the non-cool thing about this is that messing up one or a couple of the players (especially central hub ones) can send the whole metabolism out of whack. So, among other things, ASNase treatment can lead to global metabolic changes with less glycolysis (sugar breakdown) and increased use of fats for energy. Sensing amino acid deprivation, cells shut down protein-making and even activate autophagy (selective breakdown of intracellular parts) & apoptosis (programmed cell death). 

But cancer cells are tricky. Because they bypass traditional cellular “safety checks,” they can grow and divide quickly and without adequate proofreading of the DNA they copy. This allows for evolution on the really small scale – cells that randomly happen to acquire mutations that help give them a growth and/or survival advantage will out-compete other cells, so if a tumor cell happens to get a random mutation that decreases its reliance on Asn, it’ll thrive and multiply, leading to drug-resistant cancer. 

In some cases, patients on asparaginase treatment develop drug-resistance because mutations up-regulate ASNS – they start making more of the maker which they hadn’t been making. Doctors and scientists are looking into co-treating such patients with ASNS inhibitors. Additionally, they’re working to figure out what other “bypass” mechanisms the cells are using to survive and targeting those alternate routes to Asn as a supplement to ASNase treatment. For example, in a study earlier last year, Laura Hinze et al. found that some ASNase-resistant ALL cells were getting the arginine they needed by breaking down other proteins & the cells could be made sensitive to ASNase again if they prevented those proteins from being tagged with ubiquitin, a small protein that can serve as a ticket to the protein-shredder, the proteasome

The history of the ASNase/leukemia link goes back to the 1950s – In 1953, Kidd found that guinea pig serum caused regression of implanted lymphoma cells in mice. And then in follow-up studies, Broome found that the anti-lymphoma effect was coming from asparaginase. Dolowy et al. & Hill et al. tried ASNase treatment in human patients in the mid-1960s, but it didn’t really take off as treatment until the 1970s, when they were able to produce ASNase at larger scales so they had enough for large-scale trials. Those larger trials found that ASNase helped, so it has become a standard part of childhood ALL treatment, approved for medical use in the US in 1978, and on the WHO’s list of essential medicines. ASNase is also used for treating some forms of acute myeloblastic leukemia (AML).

So worldwide, you need a lot of it. Even those early trials were held up by supply – so scientists started looking for sources of lots of asparaginase to test. And bacteria are great for making lots of protein on the cheap (one of the reasons we often use it to recombinantly express proteins (stick in genes for proteins we want made and let them make it for us). But in this case, it’s the bacteria’s own “native” proteins that are isolated and used. E. coli is the main source of therapeutic ASNase and it can be injected into the muscles, under the skin, or through IV. It’s often given in a “PEGylated” form –  it has polyethylene glycol (PEG) (carbon-carbon-oxygen chains) attached to it that help with stability & help hide it from the immune system.

Still, some patients have a “hypersensitivity reaction” to E. coli ASNase – basically the patients’ immune system recognizes that the protein is foreign and sets off an immune response that not only destroys the drug that’s there to help, but also can cause the immune system to go into overdrive and cause an allergic reaction, making things even worse. If patients respond like this, they can get switched to treatment with ASNase from a different type of bacteria, Erwinia chrysanthemi which hopefully their immune system will tolerate better. Here’s a review article if people want to learn more: 

Now, as promised, the hard-core biochemistry of Asn & how it relates to Asp. Welcome fellow geeks one and all!

Atoms (the basic units of elements like carbon (C), hydrogen (H), nitrogen (N) & oxygen (O) join together to form molecules by sharing pairs of electrons (negatively-charged subatomic particles that whizz around in “electron clouds” around dense central atomic nuclei containing positively-charged protons (& neutral neutrons) tasked with reigning them in. Atoms can share 1 pair for a single bond or 2 pairs for a stronger double bond and, although most bonds only involve 2 partners, something called “resonance” or “electron delocalization” or “conjugation” allows “extra” electrons to be shared between 3 or more atoms. When they do this in a ring, we call a molecule aromatic (an example is benzene).

The most common atomic combo you see in biochemistry is carbon (C) & hydrogen (H). You can link carbons together (with H’s as a kind of filler) to form intricate “hydrocarbon skeletons” and we call molecules based on such skeletons “organic” – I called H’s “filler” here because they aren’t very reactive & they can come & go more easily than other atoms. They’re often “swapped out” for more reactive “functional groups”

And one of the most important functional groups in biochemistry is (C=O), which is called a CARBONYL. It’s so important because O pulls e- density away from the C, making it more reactive. When it’s attached to an alkyl (non-aromatic hydrocarbon) group “R” (H or C attached to Rest of molecule) on one side it’s called an ACYL & still has free side. So both Asp & Asn have “acyl” groups, but then they get uniquer names based on what the acyl is attached to. 

Attached to an O & you call it a CARBOXYL. If O’s bound to H it’s a CARBOXYLIC ACID & if that O’s deprotonated it’s called CARBOXYLATE. Aspartic acid & aspartate are the names we give to the carboxylic acid & carboxylate states of Asp, respectively.

If, however, as in the case of Asn, the acyl’s carbonyl C is attached to an N, we call it an amide. And it reacts a lot differently. N can form 4 bonds (such as in the protonated form of the generic part of an amino acid backbone). So why does this amide N only form 3? Why doesn’t it act as a base & take another proton (H⁺) like the primary amine groups of lysine & arginine do? It has to do with making molecules happy and molecules want stability.

A good source of stability is RESONANCE (delocalized e⁻ sharing – basically neighboring atoms spend what they have to to form the “normal” bonds to their neighbors & then donate the extra into a communal fund that other contributing atoms can share too). CARBOXYLATE ANIONS are highly resonance-stabilized, BUT also negatively-charged, which makes them reactive & willing to bind H⁺ (stability -> happy, charge -> unhappy).

Amides are also resonance stabilized because, in an amide, when N is only forming 3 bonds, it has a lone pair of e⁻ that can contribute to resonance. And for resonance to occur, the N has to take on a particular “geometry” (outside scope of post) that makes these e- “unavailable” for grabbing onto other things, like a proton. This resonance is also what limits rotation around peptide bonds linking amino acids – it requires the sharing molecules to lie in a plane.

This amide group is neutral w/3 bonds (no charge -> happy). It’s neutral *overall* BUT some regions are partially positive (δ⁺) and some are partly negative (δ⁻), so you stay neutral overall but have partly charged regions. And when you have differences of charge like this we call a molecule POLAR. Water’s super polar (with O pulling electrons from the H’s, making them partly positive). Polar things like to hang out with other polar things (or fully charged things) because oppositely charged regions (which attract) can hang out together. So polar molecules like Asn are considered HYDROPHILIC (water-loving) and are often found on the outside of proteins, facing the watery environment.

So Asn’s amide does NOT act as a base (doesn’t accept a proton) because: 1) the electrons that could steal a proton have their hands a bit tied up with resonance which is something that makes them stable & thus happy and 2) the nitrogen is already partly positive, so doesn’t want to add on any more charge.

But that doesn’t mean the amide can’t do other things. One thing it *can* do is act as a linkage site for sugar chains in “glycoproteins” through N-GLYCOSYLATION. We usually think of proteins & sugars as separate things, but who says you can’t mix and match?  Glycoproteins are evidence you can – different sugars can be added onto different spots on proteins (often through the N of Asp) and serve as “flags” &/or change protein properties. much more on that here: 

As you might have guessed, the name for asparagine comes from asparagus – it was first found there – and this finding (in 1806 by Vauquelin and Robiquet from asparagus juice) was the first amino acid discovery – but they didn’t know at the time that what they’d isolated was a protein letter. They weren’t looking for protein letters, they were just trying to figure out what’s in asparagus juice and they left some juice sit out when they went on a trip, came back, and found crystals of the stuff. 

You can find it in asparagus but it doesn’t give it the smell, in case you were wondering – some researchers apparently were, because they ingested a bunch of pure asparagine and then smelled their pee and it didn’t smell asparagus-y. Turns out the bad smell comes from bodily breakdown products of a sulfur compound called asparagusic acid. Some people can’t smell these because they have different versions of genes for different smell receptors. 

how does it measure up?

systematic name: 2-Amino-3-carbamoylpropanoic acid
coded for by: AAU, AAC
chemical formula: C4H8N2O3
molar mass: 132.119 g·mol−1

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉

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